+Open data
-Basic information
Entry | Database: PDB / ID: 6km1 | ||||||
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Title | Human Carbonic Anhydrase II V143I variant 13 atm CO2 | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase II / intermediate states / water network / point mutation | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Kim, C.U. / Kim, J.K. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Iucrj / Year: 2020 Title: Structural insights into the effect of active-site mutation on the catalytic mechanism of carbonic anhydrase. Authors: Kim, J.K. / Lee, C. / Lim, S.W. / Andring, J.T. / Adhikari, A. / McKenna, R. / Kim, C.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6km1.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6km1.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 6km1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6km1 ftp://data.pdbj.org/pub/pdb/validation_reports/km/6km1 | HTTPS FTP |
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-Related structure data
Related structure data | 6klzC 6km0C 6km2C 6km3C 6km4C 6km5C 6km6C 3u7cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29303.090 Da / Num. of mol.: 1 / Mutation: V143I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 364 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-BCT / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. obs: 106259 / % possible obs: 94.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.36 |
Reflection shell | Resolution: 1.05→1.07 Å / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.76 / Num. unique obs: 5079 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U7C Resolution: 1.05→29.147 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.515 / SU ML: 0.012 / Cross valid method: FREE R-VALUE / ESU R: 0.021 / ESU R Free: 0.022 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.403 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→29.147 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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